Imputation Report For Cohort: Group3

Per chromosome imputation report for cohort Group3.

Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

Cohort Metadata

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Information captured during the processing of this cohort.

Property Value
FORMAT MINIMAC2

UPLOADED 31.5.2021

Genome-Wide

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A: Alternate Allele Frequency: Genome-Wide

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 12595817 73.058
0.1 1226219 7.112
0.2 808584 4.690
0.3 620241 3.597
0.4 497181 2.884
0.5 405055 2.349
0.6 349175 2.025
0.7 293852 1.704
0.8 243313 1.411
0.9 201520 1.169
Total 17240957 100.000

B: Imputation INFO Score: Genome-Wide

Variants binned by imputation INFO score

INFO Score Count %
0.3 561146 3.255
0.4 551448 3.198
0.5 605396 3.511
0.6 913161 5.296
0.7 1583194 9.183
0.8 2726243 15.813
0.9 10273304 59.587
1.0 27065 0.157
Total 17240957 100.000

Chromosome 1

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 952070 73.3742
0.1 90296 6.9589
0.2 57511 4.4323
0.3 45806 3.5302
0.4 36970 2.8492
0.5 30766 2.3711
0.6 27010 2.0816
0.7 22246 1.7145
0.8 18491 1.4251
0.9 16389 1.2631
Total 1297555

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 43902 3.3834
0.4 43081 3.3202
0.5 46163 3.5577
0.6 68122 5.2500
0.7 118899 9.1633
0.8 208119 16.0393
0.9 767755 59.1694
1.0 1514 0.1167
Total 1297555

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 2

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1061194 73.7986
0.1 100934 7.0192
0.2 66190 4.6030
0.3 49257 3.4255
0.4 38553 2.6811
0.5 32766 2.2786
0.6 28615 1.9900
0.7 23482 1.6330
0.8 20138 1.4005
0.9 16831 1.1705
Total 1437960

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 46664 3.2452
0.4 44404 3.0880
0.5 48259 3.3561
0.6 73693 5.1248
0.7 129874 9.0318
0.8 230448 16.0260
0.9 862867 60.0063
1.0 1751 0.1218
Total 1437960

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 3

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 893321 73.3088
0.1 87404 7.1727
0.2 55484 4.5532
0.3 42770 3.5098
0.4 35788 2.9369
0.5 28640 2.3503
0.6 24740 2.0302
0.7 20378 1.6723
0.8 17000 1.3951
0.9 13047 1.0707
Total 1218572

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 37840 3.1053
0.4 36976 3.0344
0.5 39145 3.2124
0.6 60053 4.9281
0.7 107120 8.7906
0.8 193716 15.8970
0.9 741817 60.8759
1.0 1905 0.1563
Total 1218572

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 4

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 856320 71.9719
0.1 82859 6.9641
0.2 60861 5.1152
0.3 45157 3.7954
0.4 34261 2.8796
0.5 27608 2.3204
0.6 24437 2.0539
0.7 22094 1.8570
0.8 19785 1.6629
0.9 16415 1.3796
Total 1189797

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 37810 3.1779
0.4 36914 3.1025
0.5 39964 3.3589
0.6 59493 5.0003
0.7 105663 8.8808
0.8 185664 15.6047
0.9 723058 60.7715
1.0 1231 0.1035
Total 1189797

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 5

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 808850 73.3415
0.1 77360 7.0145
0.2 52426 4.7537
0.3 40314 3.6554
0.4 31538 2.8597
0.5 24209 2.1951
0.6 23148 2.0989
0.7 18261 1.6558
0.8 14898 1.3509
0.9 11851 1.0746
Total 1102855

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 34681 3.1447
0.4 33593 3.0460
0.5 36189 3.2814
0.6 55164 5.0019
0.7 97229 8.8161
0.8 172857 15.6736
0.9 671746 60.9097
1.0 1396 0.1266
Total 1102855

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 6

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 783815 72.3661
0.1 79982 7.3844
0.2 53044 4.8973
0.3 41061 3.7910
0.4 32608 3.0105
0.5 26451 2.4421
0.6 21988 2.0301
0.7 17501 1.6158
0.8 15269 1.4097
0.9 11406 1.0531
Total 1083125

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 32224 2.9751
0.4 31800 2.9359
0.5 34548 3.1897
0.6 50868 4.6964
0.7 89283 8.2431
0.8 160140 14.7850
0.9 677249 62.5273
1.0 7013 0.6475
Total 1083125

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 7

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 701088 72.6673
0.1 69085 7.1606
0.2 48053 4.9807
0.3 35763 3.7068
0.4 28942 2.9998
0.5 23261 2.4110
0.6 19280 1.9984
0.7 16554 1.7158
0.8 11929 1.2364
0.9 10837 1.1232
Total 964792

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 31238 3.2378
0.4 30318 3.1424
0.5 33144 3.4354
0.6 49818 5.1636
0.7 87033 9.0209
0.8 149827 15.5295
0.9 582043 60.3283
1.0 1371 0.1421
Total 964792

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 8

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 707357 73.9793
0.1 64852 6.7826
0.2 43730 4.5735
0.3 32685 3.4184
0.4 27580 2.8845
0.5 21377 2.2357
0.6 19512 2.0407
0.7 15419 1.6126
0.8 13091 1.3691
0.9 10552 1.1036
Total 956155

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 29802 3.1169
0.4 29582 3.0938
0.5 32711 3.4211
0.6 48336 5.0552
0.7 85032 8.8931
0.8 151981 15.8950
0.9 577344 60.3818
1.0 1367 0.1430
Total 956155

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 9

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 528874 73.1207
0.1 54463 7.5299
0.2 33701 4.6594
0.3 25073 3.4665
0.4 20598 2.8478
0.5 15719 2.1733
0.6 14483 2.0024
0.7 11939 1.6507
0.8 9644 1.3334
0.9 8795 1.2160
Total 723289

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 23237 3.2127
0.4 22937 3.1712
0.5 25199 3.4839
0.6 38708 5.3517
0.7 66675 9.2183
0.8 116885 16.1602
0.9 428770 59.2806
1.0 878 0.1214
Total 723289

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 10

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 606853 72.6499
0.1 60660 7.2620
0.2 40141 4.8055
0.3 28161 3.3713
0.4 25200 3.0168
0.5 20472 2.4508
0.6 17289 2.0698
0.7 14335 1.7161
0.8 12521 1.4990
0.9 9680 1.1588
Total 835312

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 27313 3.2698
0.4 27084 3.2424
0.5 27627 3.3074
0.6 41647 4.9858
0.7 73713 8.8246
0.8 128009 15.3247
0.9 508906 60.9241
1.0 1013 0.1213
Total 835312

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 11

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 595701 72.4771
0.1 58607 7.1305
0.2 36207 4.4052
0.3 31124 3.7868
0.4 24017 2.9221
0.5 20888 2.5414
0.6 17741 2.1585
0.7 14378 1.7493
0.8 12351 1.5027
0.9 10902 1.3264
Total 821916

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 25751 3.1330
0.4 25134 3.0580
0.5 27553 3.3523
0.6 41856 5.0925
0.7 73703 8.9672
0.8 128199 15.5976
0.9 498474 60.6478
1.0 1246 0.1516
Total 821916

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 12

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 580494 72.8946
0.1 57064 7.1657
0.2 35767 4.4914
0.3 30109 3.7809
0.4 23105 2.9014
0.5 19057 2.3931
0.6 15735 1.9759
0.7 13018 1.6347
0.8 12331 1.5484
0.9 9667 1.2139
Total 796347

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 25246 3.1702
0.4 24896 3.1263
0.5 26772 3.3619
0.6 40052 5.0295
0.7 72049 9.0474
0.8 124604 15.6469
0.9 481487 60.4620
1.0 1241 0.1558
Total 796347

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 13

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 422367 71.2972
0.1 43623 7.3637
0.2 27692 4.6745
0.3 22983 3.8796
0.4 17481 2.9509
0.5 15658 2.6431
0.6 12518 2.1131
0.7 11202 1.8909
0.8 9834 1.6600
0.9 9045 1.5268
Total 592403

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 18136 3.0614
0.4 18038 3.0449
0.5 19638 3.3150
0.6 30286 5.1124
0.7 54155 9.1416
0.8 93421 15.7698
0.9 358335 60.4884
1.0 394 0.0665
Total 592403

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 14

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 395998 72.9954
0.1 40120 7.3954
0.2 26136 4.8177
0.3 18615 3.4314
0.4 15451 2.8481
0.5 12184 2.2459
0.6 9915 1.8277
0.7 9381 1.7292
0.8 7763 1.4310
0.9 6934 1.2782
Total 542497

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 17506 3.2269
0.4 17089 3.1501
0.5 18473 3.4052
0.6 28449 5.2441
0.7 49685 9.1586
0.8 84476 15.5717
0.9 326141 60.1185
1.0 678 0.1250
Total 542497

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 15

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 339363 72.6854
0.1 33056 7.0800
0.2 21803 4.6698
0.3 16910 3.6218
0.4 14363 3.0763
0.5 11616 2.4879
0.6 8867 1.8992
0.7 7837 1.6785
0.8 6479 1.3877
0.9 6599 1.4134
Total 466893

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 15817 3.3877
0.4 15141 3.2429
0.5 17327 3.7111
0.6 25826 5.5315
0.7 44178 9.4621
0.8 74321 15.9182
0.9 273850 58.6537
1.0 433 0.0927
Total 466893

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 16

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 395103 74.0757
0.1 37742 7.0760
0.2 23073 4.3258
0.3 18918 3.5468
0.4 14203 2.6628
0.5 12136 2.2753
0.6 10739 2.0134
0.7 9402 1.7627
0.8 6835 1.2815
0.9 5226 0.9798
Total 533377

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 19104 3.5817
0.4 19031 3.5680
0.5 21464 4.0242
0.6 31130 5.8364
0.7 52178 9.7826
0.8 86962 16.3040
0.9 303082 56.8232
1.0 426 0.0799
Total 533377

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 17

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 338374 73.7251
0.1 30352 6.6131
0.2 23063 5.0250
0.3 15204 3.3127
0.4 13645 2.9730
0.5 11104 2.4193
0.6 8937 1.9472
0.7 8252 1.7980
0.8 5829 1.2700
0.9 4207 0.9166
Total 458967

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 16912 3.6848
0.4 16656 3.6290
0.5 19045 4.1495
0.6 28670 6.2466
0.7 47529 10.3556
0.8 75054 16.3528
0.9 254337 55.4151
1.0 764 0.1665
Total 458967

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 18

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 344192 72.5219
0.1 34108 7.1866
0.2 23332 4.9161
0.3 17755 3.7410
0.4 13983 2.9462
0.5 11062 2.3308
0.6 9103 1.9180
0.7 8273 1.7431
0.8 6602 1.3911
0.9 6194 1.3051
Total 474604

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 15100 3.1816
0.4 14736 3.1049
0.5 16602 3.4981
0.6 26128 5.5052
0.7 44826 9.4449
0.8 76700 16.1608
0.9 280187 59.0360
1.0 325 0.0685
Total 474604

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 19

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 263942 72.2824
0.1 29529 8.0867
0.2 18438 5.0494
0.3 13479 3.6913
0.4 9785 2.6797
0.5 8582 2.3502
0.6 6918 1.8945
0.7 6360 1.7417
0.8 4480 1.2269
0.9 3641 0.9971
Total 365154

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 12957 3.5484
0.4 13173 3.6075
0.5 14713 4.0293
0.6 23187 6.3499
0.7 37837 10.3619
0.8 58530 16.0289
0.9 203915 55.8436
1.0 842 0.2306
Total 365154

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 20

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 271018 72.8537
0.1 27448 7.3784
0.2 17896 4.8107
0.3 13748 3.6957
0.4 11178 3.0048
0.5 8795 2.3642
0.6 7740 2.0806
0.7 5917 1.5906
0.8 4647 1.2492
0.9 3616 0.9720
Total 372003

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 11905 3.2002
0.4 12235 3.2890
0.5 13559 3.6449
0.6 21169 5.6905
0.7 35938 9.6607
0.8 59715 16.0523
0.9 217232 58.3952
1.0 250 0.0672
Total 372003

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 21

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 157445 71.0742
0.1 15945 7.1979
0.2 10237 4.6212
0.3 9126 4.1197
0.4 7173 3.2381
0.5 5998 2.7076
0.6 4903 2.2133
0.7 4421 1.9957
0.8 4158 1.8770
0.9 2116 0.9552
Total 221522

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 7765 3.5053
0.4 7654 3.4552
0.5 9288 4.1928
0.6 13501 6.0947
0.7 23011 10.3877
0.8 35649 16.0928
0.9 124505 56.2043
1.0 149 0.0673
Total 221522

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 22

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 164388 73.0587
0.1 15978 7.1011
0.2 10946 4.8647
0.3 8064 3.5839
0.4 6905 3.0688
0.5 5398 2.3990
0.6 4619 2.0528
0.7 3834 1.7039
0.8 3020 1.3422
0.9 1856 0.8249
Total 225008

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 8245 3.6643
0.4 8170 3.6310
0.5 9527 4.2341
0.6 13858 6.1589
0.7 22678 10.0788
0.8 36471 16.2088
0.9 125827 55.9211
1.0 232 0.1031
Total 225008

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome X

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 427690 76.2569
0.1 34752 6.1963
0.2 22853 4.0747
0.3 18159 3.2377
0.4 13854 2.4702
0.5 11308 2.0162
0.6 10938 1.9502
0.7 9368 1.6703
0.8 6218 1.1087
0.9 5714 1.0188
Total 560854

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 21991 3.9210
0.4 22806 4.0663
0.5 28486 5.0790
0.6 43147 7.6931
0.7 64906 11.5727
0.8 94495 16.8484
0.9 284377 50.7043
1.0 646 0.1152
Total 560854

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering